Tuesday, December 8, 2020

Final US Election Results - Polling Bias Update

I created the following video for my STAT 101 class, who get to learn about the topic of sampling bias. Polling bias (the difference between what the polls said would happen in the US election and what actually happened) is an example of sampling bias, so the lecture may be of interest to a much more general audience than just my students. You can check it out here:

Friday, November 6, 2020

First Post Election Update

 I created a second video on the US election for my class, which I thought might be an interesting follow-up to my final pre-election video, which I posted on youTube and published an article on it here (with an embedded video link).

To summarize, the election is not yet called, they are still counting votes. As of this morning, my election prediction of 269 electoral college votes for Biden and 269 for Trump (see video in above linked article) is remarkably close to how things appear to be panning out. My prediction that the election is very very close appears to have been correct, which was in sharp contrast to all mainstream pollsters, who were all predicting a major Biden victory. I did think Trump was going to scrape through the electoral college system and eventually win the presidency in a long drawn out process involving Congress, this appears to not be the case. Trump is trying to fight the results in court, so that may result in drawing out the process of having an official definitive winner. I mentioned in my prediction video that it is a tight race and either candidate was in a position to win. 

I have not updated the analysis to include polling bias for 2020 as the final vote counts are not yet in. There will be more updates in the future for my class, so I will likely add more posts here as well.

Here is the video from youTube:

Monday, November 2, 2020

US Election, Polling Bias, Calling the Election

I have been tasked with teaching Statistics 101 this term, which includes the subject of sampling bias. One of the most common examples of sampling bias is polling bias, which turned out to be very important in the 2016 US election. I selected this topic as an in-depth example for my class as the 2020 election will unfold as our course does.

Towards that end, I have been updating the class throughout the term as to changes in the polls as well as what the polls would be if we were to adjust them to compensate for the known per state polling bias observed in the 2016 election. 

I promised a final update just before the election, which is found below in an embedded video. The recorded video outlines the issues I have identified that may impact the upcoming election (repeat of previous polling bias, as well as Biden's regionally lopsided support that doesn't help him). The video discusses some of the potential impact of those issues, made some preliminary predictions, and then I even take a chance on calling a possible election outcome, even though, at this point in time, statistically speaking, either candidate is in a position to win the election, assuming 2016 polling bias repeats itself (see the video). (spoiler alert: the race is wide open and my observations these past 6 weeks have inclined me towards Trump barely winning, I also outline a highly plausible scenario where he does just that). 

If you are interested, see the following video for a detailed lecture on this topic that I prepared for my class. I thought other people might find it interesting, so I decided to post it (plus I've been neglecting this site for a long time). The topic should be accessible enough to a general audience, even though I'm addressing my class.

I will find it interesting to compare the various possible outcomes outlined in the video with the results of the election that will be reported tomorrow night and intend to follow up with more posts on this topic, regardless of the outcome.

If the embedding above doesn't work, you can follow this link to the youtube page where the video is embedded from: https://www.youtube.com/watch?v=iCRFnTNBm7c&t=141s

Tuesday, June 12, 2018

Focal Cortical Dysplasia Findings

A colleague of mine has just had a new article published in the journal Brain Research (I'm third author on this paper). The study looks at patients with Focal Cortical Dysplasia, a medical condition that predisposes the patient to developing epilepsy. Our work looked at a large collection of brain MRI examinations of patients with Focal Cortical Dysplasia and compared them with a pool of typically developing participants.

Sorting Statistic Based Assessment of Group-wise Differences

I recently published an article in the Journal of Healthcare Engineering demonstrating a minor adaptation of a component from my (now rather old) PhD thesis. The technique is based on sorting statistics and is compared with the established Cohen's d statistic for assessing effect size (the amount of difference observed between two groups of samples). Cohen's d statistic assumes that the measurements available follow a 'normal' (or Gaussian or Bell-shaped) distribution, whereas the approach I developed makes no such assumptions.

Friday, June 1, 2018

Structural Development of the Human Brain - The Clinical View

Last year I published an article in the excellent journal Human Brain Mapping that analyzes a huge population of patients across a wide range of developmental ages who received clinical imaging at Boston Children's Hospital. You can check out the article here.

Wednesday, January 11, 2017

Canada Research Chair

Dr. Levman (the founder of www.spotlight-on-science.com) has recently started a new faculty position as the Canada Research Chair in Bioinformatics at St. Francis Xavier University's Department of Mathematics, Statistics and Computer Science (recently ranked the #2 computer science department in Canada by Maclean's in terms of field weighted citation impact, an indication of the department's excellent research output).

Friday, September 23, 2016

Healthy Brain Development and Multivariate MRI

Earlier this year I published a review article addressing pediatric multivariate analyses in healthy brain development with MRI. Multivariate analyses are statistical and technological methods for evaluating multiple measurements at the same time. Combinations of physiologically meaningful biomarkers (measurements) can be useful for the detection, characterization and diagnosis of a wide variety of pathological conditions as departures from expected growth trajectories of healthy brain development.

Healthy Brain Development and Multivariate MRI

Earlier this year I published a review article addressing pediatric multivariate analyses in healthy brain development with MRI. Multivariate analyses are statistical and technological methods for evaluating multiple measurements at the same time. Combinations of physiologically meaningful biomarkers (measurements) can be useful for the detection, characterization and diagnosis of a wide variety of pathological conditions as departures from expected growth trajectories of healthy brain development.

Monday, March 28, 2016

Multivariate Analyses in Neurodevelopmental Disorders

I recently published an article on the use of multivariate analyses in neurodevelopmental disorders among pediatric populations receiving brain MRI examinations. This review article covers the state of the research literature on developmental disorders such as autism, attention deficit hyperactivity disorder, epilepsy, cortical dysplasia, schizophrenia, etc. for studies that include multivariate analyses. Multivariate analyses are such that they involve the simultaneous assessment of multiple variables at the same time (normal studies will only consider each measured variable individually). Since many measurements are obtainable from a single MRI examination, multivariate techniques have the potential to identify combinations of underlying physiological conditions associated with a variety of different neurodevelopmental disorders.

Monday, September 14, 2015

Identifying poor outcomes in autism as early as possible

A recent study on autism [1] was featured in the popular journal Science [2] and presented functional brain imaging patterns associated with autism subjects who have poor language outcome. Early identification of autistic subjects with poor outcomes is an important research avenue with the potential to assist in informing patient care by steering treatment decisions, observing disease progression and monitoring therapeutic response. It is encouraging to see such considerable potential from functional magnetic resonance imaging (MRI) of the brain and it should also be noted that MRI is capable of acquiring a wide variety of different physiological measurements. I was fortunate to get a short letter/comment published with the journal in online format discussing the potential to further characterize autism and to potentially identify those subjects with poorer outcomes using pH sensitive MRI [3] and machine learning technologies. I introduce the reader to this topic here:

Friday, September 11, 2015

Contrast Agent Diffusion Inspired Breast Cancer Research

I've recently had an article published in the Journal of Digital Imaging focused on a biomarker that may be able to assist in the characterization of breast cancer from magnetic resonance imaging (MRI) examinations. 

Wednesday, September 9, 2015

Neurodevelopmental Research at Harvard

I've recently started a new research position at Boston Children's Hospital, Harvard Medical School focusing on neurodevelopmental brain research. I am interested in many topics in this domain and have been focusing on research applied to the imaging of autism with both magnetic resonance imaging (MRI) and magnetic encephalography (MEG). This website has not been updated in some time due to the challenges I've faced in securing my new research position and moving my family from Oxford, UK to Canada (temporarily) and then onwards to the Boston area. New articles discussing some of my recent scientific publications will be published soon.

Additionally, I have multiple research papers from my previous position at the University of Oxford on stroke imaging with MRI which are being revised towards eventual publication.

Jacob Levman, PhD
Boston Children's Hospital
Harvard Medical School

Friday, October 24, 2014

Comment on Breast Cancer in Science

I’ve just had a small comment on breast cancer published on Science’s website. The comment is in reply to an interesting article discussing over-treatment in ductal carcinoma in situ (DCIS: a type of cancer that is contained in the milk duct). My comment is reprinted below. Unfortunately Science’s website submission system mucked up some of the letter (formatting etc.) but no matter as it can be read here:

Monday, October 13, 2014

Machine Learning for Semi-Automatic Segmentation of Breast Lesions from MRI

I have recently had another journal article published on machine learning. This one is focused on a machine learning formulation I developed as a simplification of a technique I published earlier on - you can access information on the earlier publication here. The technique I have just had published (accessed from here) is a machine learning based tool for radiologists allowing them to delineate (or segment) a suspicious lesion from a breast MRI examination with a few seconds of user interaction to define tissue they are interested in analyzing further and tissue that is not of clinical significance.

Thursday, June 19, 2014

pH Imaging in Stroke

I recently published a preliminary study on stroke imaging at the International Symposium on Magnetic Resonance in Medicine (ISMRM), the main MRI researchers' conference which was held in Milan, Italy.

Sunday, December 1, 2013

Longitudinally Evaluated Disease Screening Technologies

I've recently had another journal article published. It is focused on the evaluation of disease screening technologies in longitudinal trials (ie. long running research trials which rely on a new technology for monitoring a population). As a technology researcher, I am particularly interested in this subject as I endeavor to develop new disease detection technologies which will be evaluated in longitudinal trials. The article was published in the Journal of Clinical and Diagnostic Research and you can access it here.

Friday, July 12, 2013

Machine Learning in MRI-enabled Breast Cancer Screening

I've just had another research study published, this time in the Journal of Digital Imaging and has just been published online ahead of the print edition. The article presents a mathematical formulation to the supervised learning problem and demonstrates its application in the computer-aided diagnosis of breast cancer from MRI screening examinations of high-risk women. The article is copyrighted by Springer, the journal's publisher, so I can't reproduce it on Spotlight-on-Science, however, you can access it from their website here.

Sunday, June 2, 2013

Mortality Among Women Enrolled in MRI enabled Breast Cancer Screening

I've just had an article published in the journal Radiology focusing on the mortality/survivorship results of MRI-enabled breast cancer screening. It takes a very long time to acquire mortality/survivorship data in a breast cancer screening study. Typically a population is followed for a long time (often more than 10 years) in order to establish what percentage of women who develop breast cancer go on to survive the disease many years after a diagnosis from the screening method being tested.

Sunday, March 17, 2013

The Significance of Statistical Significance

The other year I authored a paper that takes unique approaches to demonstrating that the commonly used term for statistical significance (p < .05) is obtainable from data that is not 'significant'. The paper was invited for publication in a new journal, but at the time I was too busy focusing on other endeavours to develop the paper and take advantage of the publication invitation.

Friday, February 8, 2013

Clinical Computer-Aided Detection in Breast Cancer Screening

I've authored a meta-analysis on the clinical use of computer-aided detection technologies in x-ray mammographic breast cancer screening. A meta-analysis is a type of study where the scientist analyzes the literature on a particular subject. I am a young researcher and meta-analyses are typically authored by well established and senior scientists. Furthermore, the subject matter of the study is both clinical and technical making an appropriate place for its publication somewhat elusive.

Tuesday, January 29, 2013

Overfitting in Computer Aided Diagnosis

I've just had the honour of having one of my journal papers published by invitation. The paper is on overfitting, a scourge of a problem for pattern recognition researchers. Overfitting is a problem that occurs when a learning machine is overly tuned to the data it was provided to learn on. Overfitting is a particularly problematic phenomenon as an overfitted classifier (or supervised learning algorithm) may yield extremely promising results on the data set being evaluated while simultaneously providing an unreliable test on new datasets that it has not yet been exposed to.

Friday, October 26, 2012

Stroke MRI at Oxford

It has been a while since I have updated Spotlight-On-Science with a new posting. I have been busy working at the University of Oxford on a research position combining advanced computer applications and MRI.

Tuesday, April 10, 2012

Scientists vs. 100 Monkeys

What is a p-value?  Scientists are regularly tasked with the job of demonstrating that their experimental results are significant and to do so they test for statistical significance (and insert things that look like this in their studies:  p < 0.05) but what does that mean?

Wednesday, December 21, 2011

Reinterpretation on Negative Findings for CAD in Mammography

I have recently published an article in the Journal of the National Cancer Institute (Oxford University Press) a leading medical journal. It is a letter in reply to a recently published and highly publicized study on the use of computer-aided detection (CAD) technologies in breast cancer screening via mammography. That study, published late last summer was the world's largest study on the effects of computer-aided detection technologies in breast cancer screening (in terms of the number of examinations incorporated into the analysis - 1.6 million screening examinations). The study reported largely negative findings for the performance of breast cancer screening with the help of computer-aided detection technologies.

Thursday, October 6, 2011

Site Update: Nature Blogs

This website was originally founded under the name With A Grain of Salt and was eventually listed with Nature Publishing Group's network of independent science themed blogs / websites (you can check out their network over at blogs.nature.com). More recently I have revamped this website to look more professional and renamed it Spotlight on Science. Under the new name, this website has been re-included into Nature Publishing Group's network of high quality independent blogs.

Tuesday, October 4, 2011

Detecting Breast Cancer by Assessing the Lesion's Margin

I recently published an article with the journal Academic Radiology. The paper presents a method for assessing a tumour's margin towards the detection of breast cancer from state-of-the-art MRI examinations. Malignant margins tend to appear diffuse and variable by virtue of cancerous lesions being characterized by invading into neighbouring tissues. Margin measurements also have potential applications in the assessment of whether a lumpectomy (removing a lesion via surgery)   actually successfully removed the entire tissue of interest, however, this article is focused on using the margin measurement towards a more accurate diagnosis of breast cancer from MRI examinations. 

Thursday, September 29, 2011

Statistical Significance and the Publication Process

In theory if you have an original presentation of data, or an original collective argument on a given scientific topic then, in order to get your ideas "out there" and heard among other scientists you submit your work to the peer review process. If the peer reviewers agree that the work holds merit then the work will be published. Unfortunately this publishing paradigm is an idealization - with journals commonly making subjective decisions as to what should be sent out for peer review.

Friday, September 9, 2011

On Digital Infrared Thermal Imaging for Breast Cancer Detection

I recently got a letter published in the British Medical Journal on Digital Infrared Thermal Imaging for the detection of breast cancer. Since no copyright is taken out on these letters, I am reproducing it here:

Tuesday, August 23, 2011

Update: News on the Nature Front

I have good news, I am now part of the editorial board for Nature's Scientific Reports. I will be in charge of the peer review process for research papers in biophysical and computational methods in cancer research (etc.). The journal removes the subjective decision of how significant a research study appears to be in order to be worthy of publication (which is great!). Instead the publication of papers is contingent upon being technically and scientifically sound as well as original.

The journal is put out by the extremely successful Nature Publishing Group and is also open access - of which I am also very supportive. This allows all research studies published at the journal to be read by anyone in the world (who has the luxury of an internet connection). I look forward to performing my duties as an editorial board member and also look forward to publishing some of my work with them.

Jacob Levman, PhD
Imaging Research
Sunnybrook Research Institute
University of Toronto

Wednesday, August 10, 2011

Not All Computer Aided Detection Methods Are Equal

A recent publication in the Journal of the National Cancer Institute has indicated that computer-aided detection (CAD) technologies do not aid in improving breast cancer detection via x-ray mammography based screening (here is a news article on the publication). The conclusions reached in this study may be flawed and this article explores some of the issues of why this may have occurred.

Wednesday, June 1, 2011

Chronic and Recent Starvation and Malnourishment

I recently got a relatively short article published on malnourishment with the European Journal of Public Health which is published by the Oxford University Press. The article is titled "Chronic and Recent Starvation and Malnourishment" and is accessible from the journal's website here. If you would like to read the article, I am reprinting it below:

Monday, April 25, 2011

Comparing Screening Methods in Long Term Analyses

I recently got an article published with the European Journal of Public Health, which is put out by Oxford University Press. The article comments on methods for evaluating disease detection (or screening) methods after many years in a longitudinal analysis. Disease detection rates are one of the most common evaluative methods in this scenario and my article explains why that can be an unsafe evaluative method that can lead to the dismissal of newer and beneficial technologies.

You can read the article by clicking here.

Wednesday, March 9, 2011

Humorous Aside: Trust Me I'm a Doctor

When I was a little boy I had a favourite T-shirt. I remember being an idealistic little kid and when asked what I was going to do with my life I said: "I'm going to cure cancer". Now I'm 32 and I'm a doctor - incidentally I earned my doctorate in breast cancer detection - one of a gazillion possible research areas that can theoretically help with the fight against cancer. 

Monday, March 7, 2011

The Problems with Evaluating Detection Technologies with Disease Caught in the First Round of Screening

My research is focused on breast cancer screening methods, however, the ideas presented here apply to the detection of most diseases.

Friday, February 11, 2011

Humorous Aside: Chutzpah in Science, part 2

Chutzpah is a Yiddish word meaning: impressive cheekiness, brash, informal shameless audacity.

Thursday, February 10, 2011

Malnutrition and HIV in Ugandan Children

I recently read a Nutrition Journal study from 2006 on severely malnourished children with and without HIV. It was a very interesting study on an extremely important topic. I am not only particularly interested in the subject of malnourishment but I’m also particularly interested in Uganda, a country where I have visited with my wife who did some of her health professional training (in Occupational Therapy from the University of Toronto) at a hospital in Mbarara.

Sunday, February 6, 2011

Humorous Aside: Chutzpah in Science

Chutzpah is a Yiddish word meaning: impressive cheekiness, brash, informal shameless audacity

Monday, January 24, 2011

Site Update: Nature Publishing Group Network

This website (formerly With a Grain of Salt) has been added as part of the Nature Publishing Group's network of science-themed independent websites (blogs). Entry is dependent on the opinion of Nature Publishing Group along with the results of an election where existing bloggers admitted into Nature's network are given a vote on new entries. I have since renamed this website Spotlight on Science and given it a more professional layout.

Friday, January 21, 2011

The Ideal Scientific Journal

In the world of science, a journal's quality is typically measured with what's called an Impact Factor. The impact factor is really a measurement of how often any given article published in a particular journal gets cited in other scientific contributions. Journals with high impact factors tend to generate a lot of citations for each of their articles and tend to be quite prestigious.

Thursday, January 13, 2011

The impact of the impact factor on the scientific publication process

The impact factor is a measure of how often articles published in a given scientific journal get cited by other research articles. Scientists tend to use the impact factor as the main method for evaluating the quality of a given journal publication. Because the impact factor is the main source of respectability for a given journal publication among scientists, journal editors are naturally biased towards achieving as high an impact factor as possible for their journal. This bias leads to a connected bias: the rejection of studies for which the journal editor qualitatively believes that the study is not likely to generate citations from other scientific research in the near future.

Tuesday, January 11, 2011

Challenges in estimating the increase in the death rate among the malnourished

A 10-year-old and largely ignored United Nations report estimated that malnourished people die at a rate of about 36 million people per year, accounting for about 58% of worldwide deaths. Proper statistics aren't kept in many of the world's countries, so we don't know if this estimate is correct. However, even if the true value is quite substantially lower, this problem is still of massive proportions. I previously published an article that helps to wrap your head around the scope of the problem by comparing the number of deaths of malnourished people with the number of deaths due to World War II (by these estimates there are about 3 times as many deaths among the malnourished as compared with deaths due to World War II).

Saturday, January 8, 2011

Humorous Aside: Peer-reviewed rejection

Peer reviewed rejection can be one of the most frustrating things about being a scientist. Here's some peer reviewed rejection humour with the hope that it can be cathartic for some scientists out there.

Thursday, January 6, 2011

The old food crisis, the chronic food crisis and the coming food crisis?

In 2008 the price for many basic foods increased dramatically. This led to rioting in many countries such as Haiti, Bangladesh, Egypt and many African countries. This chaos and the strains that the food price increases have caused on the world's poor were dubbed a "food crisis", which it surely was. However, older reports from the United Nations claim that the death rate for malnourished people is ridiculously high - 3 times higher than the death rate due to World War II. Even if this is an exaggeration, then this is still a ridiculously large problem, large enough that it deserved the title "food crisis" long before we were using that term in 2008. As such I refer to the ongoing problem as the chronic food crisis.

Tuesday, January 4, 2011

There are more benefits from breast cancer screening than simply saving a woman's life

This past year saw the eruption of a fresh controversy in breast cancer screening. The United States Preventive Services Task Force (USPSTF) issued a report to the Obama administration advising against x-ray mammographic screening for women in their forties. The journal Science reported on the controversy and published a reply letter which was also published here at Spotlight-on-Science. The article pointed out that the USPSTF task force accepted a particular conservative estimate about the number of women in their forties that needed to be screened by x-ray mammography in order to save one life (1900 need to be screened by this estimate). I pointed out that when a fully developed screening program is applied to a large population such as the United States, the use of screening still adds up to many lives saved.

Saturday, January 1, 2011

P=NP and the million dollar mathematics prize

The Clay Mathematics Institute in Cambridge Massachusetts is providing a one million dollar prize for the first person who can prove or disprove the P=NP problem. A variety of descriptions of the P=NP problem are available. Simply put, computer scientists have divided computer problems into a series of categories which include P (problems that are relatively easy to solve) and NP (problems that are relatively challenging to solve). The majority of computer scientists believe that P != NP (P is not equal to NP - this expression is repeated below) indicating that many believe problems exist which are too complex to solve for them to ever be classified as P type problems. Recently Vinay Deolalikar of HP labs released a possible proof that P != NP. His work has been subject to some criticisms, however, I am inclined to agree with his goal of proving that P != NP and good luck to him in responding effectively to his critics - that million dollar prize would sure be sweet!

Thursday, December 23, 2010

Volcanos, the sun and recent climate coolness

Europe has been experiencing unusually cold weather with many flights delayed around the continent. Over here in southern Ontario (Toronto, Canada) we've been experiencing an unusually cold December as well. The environment is a great interconnected web, thus a temperature change can not necessarily be attributed to only one cause, but is likely the result of a series of factors.

Possible contributing factors include the recent large volcanic eruption in Iceland. Click to enlarge this gorgeous picture of the Icelandic volcano (Credit R. Th. Sigurdsson):

Monday, December 13, 2010

How many dimensions are there in the universe?

Theoretical physicists regularly disagree regarding how many dimensions exist in the universe. Some put it at 10 or 11 or 13 dimensions but no one really knows how many dimensions exist in the universe. Some theoretical physicists can be quite passionate about their particular belief in the total number dimensions in the universe even though they know that they don't know what the truth is regarding the true number of dimensions.

Thursday, November 25, 2010

Breast cancer screening for women in their forties

Breast cancer screening for women in their forties has become a hot topic recently because some scientists have argued that the harms outweigh the benefits. A recent article in the journal Science (Marshall, Brawling over mammography, 2010) discusses this issue and presents some scientist's points against screening.

Monday, November 22, 2010

Google Alerts - A scientist's unsung friend

For a while now I have been experimenting with using Google Alerts as a tool to help me in research. For those who don’t know, Google Alerts is a simple application that will e-mail you whenever it finds a new page on the internet containing the search words that you provide.

Sunday, November 21, 2010

Preoperative MRI can be used without increasing mastectomy rates

RSNA (Radiologists' Society of North America) holds a gigantic radiologists conference every year in Chicago. This year's conference starts one week from today and apparently one of the presentations on the first day will be from Fabio Chiesa and colleagues from the University of Milan's School of Medicine. Apparently they will present data from 2003 to 2008 showing that preoperative MRI examinations of the breast do not necessarily cause increases in mastectomy rates.

Wednesday, November 17, 2010

Brief: MRI lowers the mortality of women at high risk for breast cancer

This is very exciting news. The New York Times has just begun reporting on a study published in the Journal of Clinical Oncology. Dutch researchers monitored a group of over 2,000 women at high-risk for breast cancer with magnetic resonance imaging technology (MRI). After 6 years of follow up only 4 of the very high risk patients (BRCA mutation carriers, 50-85% lifetime risk) died and 100% of the moderately high risk patients (15-50% lifetime risk) survived. The author's compare their impressive results with other studies which showed that 5 year survival without MRI based detection yields a 74% survival rate.

Statistical significance is not the same as significance

There is a lot of confusion among scientists regarding the appropriate use of statistics. A recent short letter on statistics published in the Canadian Medical Association Journal (CMAJ) helps illustrate this problem. CMAJ does not take out a copyright on the letters so we're reproducing it here, although you can access it directly from their website.

Friday, November 5, 2010

The chronic food crisis

The chronic food crisis has been the subject of numerous articles on Spotlight-on-Science.

Tuesday, November 2, 2010

Humorous Aside: The nature of scientific mistakes

Mistakes are part of the nature of scientific research.

Humorous Aside: The changing face of peer-reviewed publications

The process of getting one's research published has changed dramatically over the years. When Einstein was a young man he didn't have a PhD and was working in a patent office. He was brilliant, and managed to get multiple research papers published in Physics journals even though he didn’t have a PhD nor an academic appointment. He was the ultimate outsider.

Friday, October 29, 2010

Evaluating magnetic resonance mammography

Breast cancer detection can be a contentious area of debate. A recent article published in the British Medical Journal is presented here. The article acts as a reply to an article written by Dr. Kell who argued that MRI was providing no benefits to patients who've already been diagnosed with breast cancer. My reply points out that cancer detection rates are not necessarily a good way to evaluate a new screening method after years of monitoring a population (ie. in longitudinal studies). It sounds counter-intuitive but the reasoning is simple: If you're monitoring a population and you add a new screening method that is more sensitive, then it picks up more tumours as it is initially applied but by catching those tumours it has created a population that has fewer tumours remaining which lowers the cancer detection rate. Thus comparing cancer detection rates after years in a longitudinal study might be a very bad way to compare the efficacy of a new screening method! Surprised?

Thursday, October 21, 2010

Unnecessary testing and thermography

Spotlight-on-Science recently wrote an article about the problems with thermography – you can check it out here. At present many companies exist which offer breast cancer screening by thermography (taking a simple thermal image of the surface skin of the breast), however, finding a medical doctor / radiologist who is equipped to interpret the thermogram image is much harder (and an absolutely necessary step for thermography to be useful to the patient). Unfortunately, thermography has been shown to have a terrible sensitivity to catching cancer though it has received a lot of hype.

Wednesday, October 20, 2010

News Brief: Hunger Still at Astronomical Levels

Recent news reports have indicated that the number of hungry people in the world has dropped to 925 million - down from just over 1 billion.

The cause of the decline was primarily attributed "to better economic prospects in 2010 and the fall in food prices since mid-2008."

Monday, October 18, 2010

Humorous Aside: Einstein's inspiration?

Einstein gave us so many scientific contributions. Not the least of which was a relationship between energy and matter and insights into the nature of time.  I wonder if his inspiration for these theories went through any stages like this:

Thursday, October 14, 2010

Hunger deaths comparable to World War 2 deaths

I decided to write this article and put it on my blog for World Food Day. Maybe I’m a dreamer but it would be great if one day we lived in a world where no one went hungry.

No one knows for certain how many hungry people die every day but according to United Nations figures, malnourished and starving people are dying 3 times faster than people were dying on an average day of World War 2! Chronic mass starvation and malnourishment deaths are not well reported – they are not typically considered newsworthy because by many people's thinking they are not news if they are a chronic problem (news being something that's new, chronic problems being something that’s old). The lack of worldwide knowledge of the scale of this problem is staggering. Even if the United Nations’ published numbers [1] are grossly exaggerated, the problem is still of massive proportions.

Wednesday, October 13, 2010

Be cautious with thermography

The Huffington post recently published an article by a medical doctor on the greatness of thermography as a mechanism for breast cancer detection, you can access it here.

As a breast cancer researcher, I took issue with this article because it was written by a medical doctor and provides women with some highly questionable advice (for instance: "Thermography is a better technology [than mammography]"). Dr. Northrup does not appear to be equipped to determine which technology (mammography or thermography) is better. Dr. Northrup’s main reason for believing that thermograms are the best in breast cancer detection is because of this very old study (30 years old in fact):

Monday, September 13, 2010

New developments in statistical machine learning research with application to breast cancer detection

Article on a new statistical machine learning technique recently published and presented. The technique's abilities have been demonstrated in breast cancer detection from state-of-the-art MRI examinations.

Monday, August 23, 2010

September 11th

A short article on peculiar personal effects of September 11th and an interesting technical conference in Argentina.

Friday, August 20, 2010

Humorous Aside: Che Guevara and the capitalist comeback

Just when you thought Che Guevara's reach couldn't extend further into modern capitalist society:

Thursday, August 5, 2010

Humorous Aside: Governments unite against free communications

Research in Motion's blackberry is being banned or having its communications restricted around the globe because its communications equipment is too secure for a repressive government to see what its citizens are saying to each other. It is happening in the United Arab Emirates, Saudi Arabia and Indonesia - you can check it out here. (August 12th addition: India just added itself to this list of nations trying to restrict communication freedoms)

Thursday, July 29, 2010

Wednesday, July 21, 2010

Humorous Aside: What's new pussycat?

I recently read in the news (the globe and mail) that in Indonesia they have a delicacy called Kopi Luwak which is a special kind of coffee prized for its smoothness.

Tuesday, May 18, 2010

Pre-censored in China

It was recently discovered that this website comes pre-censored in China. The website is hosted by Google's free service which apparently has long been censored in China. It would seem that the Chinese Communist government doesn't like it that anyone can create a website in this space and write anything they want!

Saturday, January 9, 2010

Preventing cancer and other problems with alkaline pills?

Cancer cells proliferate in acidic environments. A healthy human is free of cancer and is not acidic (typical healthy pH is slightly basic: 7.4). But it is common for people to have unhealthily low pH levels (more acidic).

Wednesday, January 6, 2010

Creating money

An article on the peculiarities of the ways we create money.

Friday, January 1, 2010

Global warming and global cooling

When volcanos erupt it lets off a bunch of gases into the atmosphere. A big volcanic eruption can actually cause global cooling - light waves that would otherwise have reached the earth's surface and caused some warming were instead deflected by particles in the atmosphere put up there by the volcanic eruption. When we burn some fuel, greenhouse gases are emitted which are known to act as an insulator for the earth (helping us to stay warm by retaining heat).

Bringing democracy to the United Nations

A short point on obvious shortcomings at the United Nations.

Wednesday, December 30, 2009

How much climate change is connected with the solar cycle length?

There is a big controversy in climate science regarding the magnitude of the effect of solar variations on the earth's climate. This article discusses one of those controversial theories.

Saturday, December 26, 2009

Brief: Investing in the price of food

When a trader buys food products (grains etc.) on the world markets in the hopes that the price will increase they do a huge disservice to poor people in poor nations who have difficulty finding enough money to purchase basic foods such as bread.

Friday, December 25, 2009

Improving government revenues

From a US Statistical Abstract: there are about 75 million homes in America with about 48 million mortgages. At an average value of just over $100,000 the total amount of money borrowed in the form of mortgages is 5.4 trillion dollars.

Thursday, December 24, 2009

Funding for fighting climate change and world hunger

Fighting climate change is thought to be important because if we don't then some regions may produce less food and water in the future and more people will die from starvation and dehydration. No one wants starvation and dehydration to get worse.

Currently we spend about 3.7 billion dollars a year trying to feed the world through the UN World Food Programme. It was recently announced that the U.S. would commit to a climate change fighting plan which involves (eventually) contributing 100 billion dollars per year to dealing with the problem.

Tuesday, December 22, 2009

An inconvenient truth

The earth is filled with problems: war, terrorism, climate change, crime, starvation, etc. It can be very difficult to properly assess which problem facing the world is the most poignant and thus the most deserving of our attention and resources, however, food and malnourishment problems appear to be monumentally large.

Food waste and world hunger

I’ve heard that the world produces enough food to feed everyone. Unfortunately there are 1 billion malnourished people in the world today (according to the UN World Food Programme). The following article presents a quick rough estimate of food waste and compares it with how much food might be needed for the world’s malnourished people.

Friday, December 18, 2009

Follow up on climate change funding

The dangers climate change presents can be described as follows: if in the future the world is significantly hotter then some regions may not produce as much food or water as they currently do and this can lead to drought, starvation and dehydration. Furthermore, many scientists have pointed out that climate change is likely to cause more episodes of extreme weather conditions. Extreme weather patterns (like say a tsunami or hurricane) can appear quite quickly and can have devastating effects on the local population’s ability to feed itself. This is all the more poignant in poor countries where the local populations tend to lack adequate financial resources.

Thursday, December 17, 2009

Funding to fix climate change and making sure the world doesn’t go hungry or thirsty

Today in the news it was announced by Hillary Clinton (secretary of state for the Obama administration) that 100 billion dollars per year was what the Americans were offering as part of a multinational deal to help fight climate change.

Tuesday, December 1, 2009

Brief: Government spending and world hunger

Many of the world's governments are willing to spend billions of dollars in the cause of fighting climate change. The world's governments are willing to spend hundreds of billions of dollars to make sure that their banking institutions and insurance companies don't go bankrupt (out of fear of causing a prolonged recession / depression). When at war nations are willing to spend obscene amounts of money waging them.

Saturday, November 28, 2009

Banks and collusion in Canada

When the economy got bad and the Canadian bank's bottom lines started looking slim they decided to steal from their customers! Many of the main banks raised the interest rates they charge on their customers in unison early this year (which is probably an example of a violation of collusion laws). The banks decided to blindly steal from everyone right when the economy was worsening and many people really were struggling.

Saturday, October 3, 2009

Jews and Muslims and the weirdness of history

History is a fascinating social science. Just about every civilization and culture that has had contact with another have also experienced inter-cultural friction. Among the bristlier subjects along this vein are the struggles between Jews and Muslims and the emotions these subjects evoke in so many.

Considering the fundamental similarities between the religions (monotheistic belief in God and a common spiritual ancestory) it is remarkable how there are types from either of these faiths (or any faith) who focus purely on the differences between their religious traditions and those of others. Many people in today's world appear enthralled to the idea that the world's religions are necessarily in conflict with each other.

In reading I have come across a few tidbits in history that I thought I might share as they might have the ability to show people the big picture: that there were times in the past when the two communities cooperated together - and hopefully this will help inspire some people to believe that it is still possible for the two communities to cooperate.

Science and physics studying consicousness and God

Physics attempts to explain the universe around us. The universe is broken down into explainable equations and relationships based on a few basic principles that attempt to explain the nature of the universe. In standard physics, explaining the universe has typically been limited to explaining matter (and the fundamental forces that govern their interactions). Very few attempts have been made that try to incorporate other known natural phenomena of the universe - like consciousness - into a mathematical or physical model of the universe. I have never heard a convincing explanation for the phenomenon of consciousness that is based purely on our understanding of matter and the fundamental forces that govern matter's interaction.

Monday, September 21, 2009

The economics of charity

A short wishful article on the need for larger scale charitable integration with existing capitalism.

Sunday, September 13, 2009

Humorous Aside: The Far Side

The Far Side is a great comic! You can check it out here. I collected a few of my favorites below.

Tuesday, September 8, 2009

Science assisted enlightenment

Buddhist texts have it that Buddha instructed monks that they could achieve advanced states of awareness through meditative practise that achieves a mental state sometimes described with the term single-pointedness - often achieved by focusing on the sensation of air currents on the nostril area (in Hinduism this is called anapana sati and is said to be able to provide liberation or moksha to the practitioner).

Monday, September 7, 2009


Homosexuality has been observed throughout the animal kingdom. Everything from elephants to dolphins to birds have been observed engaging in homosexual behaviour. There is plenty of evidence for the existence of genes that predispose the carrier to homosexuality. From an obvious Darwin - pass on your genes perspective being gay (thus probably/possibly having a pair of recessive gay genes) would not seem like a winning combination for the mere passing on of one's genes. This is one of the main reason based arguments against the naturalness of homosexuality - others don't accept it because of the dogma of some old text (such as the bible).

However, homosexuality is observed throughout the animal kingdom thus is quite natural and normal.

Thursday, September 3, 2009

Humorous Aside: Professor or worse?

A professor is a nice cushy job - assuming one has tenure. The following cartoon from PhDComics.com compares a professor with a most unusual alternative career path.

Humorous Aside: Paid too little to lose one's job?

Some funny comics from PhDComics.com.

Tuesday, August 25, 2009

Humourous Aside: Grad School and moving towards a post-doc

Some funny cartoons from PhDComics.com on entering the post-doctoral research phase of academia.

Sunday, August 16, 2009

Buddhism and the Dalai Lama

Buddhism is often referred to as a science of the mind, where principles are accepted or rejected based on the mental reactions they elicit in the practitioner. Principles are also accepted or rejected based on the perception of how closely and accurately they reflect the teachings of Siddhartha Gautama (the historical Buddha who lived ~2500 years ago on the Indian Subcontinent). By personal experience I would say that the correct application of logic is inclined to elicit a positive mental reaction in the practitioner.

Thursday, August 6, 2009

World religions and predestiny

Reason can be used to support the concept of predestiny, an example of which is demonstrated as follows: What happened in our past was fixed (the thoughts we had, the actions we took etc.). In the present we can choose to do this or that but go a moment into the future and we can look back at what we just called the present and see that we chose to do one particular thing in that moment. Thus although we supposedly have a choice in the present, there is only one thing in the present that we are actually going to choose to do. Thus it would appear that all our choices/actions were/are predestined. 

Wednesday, August 5, 2009

Einstein, light and the photoelectric effect

Einstein has blessed us with a huge quantity of scientific contributions. I'm a huge fan of the ideas he was presenting with relativity. He has also furthered our understanding of some of the properties of light. However, Einstein also said some strange things regarding the energy of light in trying to explain the photoelectric effect.

Wednesday, July 22, 2009

Humorous Aside: Intrinsic angular momentum

Quantum theory has some unusual ideas. A particularly unusual one is that a subatomic particle has an intrinsic angular momentum. The idea is as such:

any given sub atomic particle is spinning
however, the amount that particle is spinning never changes

Tuesday, July 14, 2009

Heisenberg's uncertainty principle

Heisenberg's uncertainty principle states that we cannot know certain pairs of physical properties such as a particle's position and momentum precisely and simultaneously.

Monday, July 6, 2009

Detecting cancer with MRI based pH imaging

It is known that cancerous tumours tend to exhibit acidic pH levels. In fact the urine of patients with advanced cancer can be extremely acidic. It is plausible that the acidity of cancerous tissues is detectable via MRI when the tumour is still very small.

Tuesday, June 30, 2009

Humorous Aside: Funny Farside cartoons

I love the farside, special thanks to Gary Larson for producing such a hysterical cartoon as the Far Side.

Monday, June 29, 2009

Buddhism and the permanence of matter

The Dalai Lama (the spiritual leader of Tibetan Buddhism and one of the world’s most prominent Buddhists) has indicated that he believes that Buddhism is ready for scientific analysis in the age of reason. I agree with this assessment – indeed I believe all the world’s religions need to be ready for scrutiny and analysis in the age of reason. To this end the Dalai Lama has indicated that Buddhist scriptures disproved by modern science should be abandoned.

I was thinking about how some ideas from science may conflict with the idea of impermanence which plays a moderately prominent role in some Buddhist texts.

One example may be whether matter as we know it is permanent or impermanent.

Monday, June 15, 2009

String Theory

String theorists claim that the universe has 9, 10, 11, 13 or whatever number of dimensions (depending on which theorist you talk to). These claims are based on nothing more than mathematics, however, I wouldn’t be surprised to discover that the universe does indeed have more dimensions than the 4 dimensional space-time that Einstein’s general relativity implies.

Sunday, June 14, 2009

Another Bohring article?

Problems with the Bohr model of the atom: it claims that the reason the electron does not degrade and collapse into the nucleus is because the electromagnetic force pulling the electron in is balanced by the centripetal force from the kinetic energy of the electron (moving really really fast around the core). The problem with this model is that maintaining its super fast speed is the only thing that keeps the electron from degrading into the nucleus and letting off a LOT of energy (Einstein's E=mc^2). The universe has been around for some 14 billion years, I think matter is a little more stable than that!

Saturday, June 13, 2009

Unknowns in the strong force

The electromagnetic force repels same charged particles and attracts oppositely charged particles. Similarly, the strong force attracts same charged particles

Friday, June 12, 2009

Humorous Aside: The significance of scientific research?

Once a scientist's experiments are complete (measurements taken, data collected) the scientist is typically expected to show that their research is statistically significant. A previous article shows that the main statistical significance test that people use was created in a beer factory over a hundred years ago and was only used on sets of up to 10 samples (way too few by today's scientist's standards). If you collect a lot of samples, the test will almost always give you the significance you're looking for. Luckily I discovered a new statistical significance test on the internet that will allow us to compute a number to determine if our research was worth anything (thank you PhDComics.com).

Thursday, June 11, 2009

Science assisting world peace

Science and technology have been advancing at a remarkable pace. One large contribution to changing our lives is the cell phone - not least of which because modern versions have the ability to take photographs and capture video clips.

MRI: Why do some things ring and others not?

As mentioned on previous posts MRI works because a proton in a strong magnetic field will polarize. We use it to image hydrogen along with a collection of isotopes (somewhat irregular configurations of matter where the nucleus has an unusual number of protons or neutrons). However, other than hydrogen, magnetic resonance has not been reported in all the remaining elements (just isotopes). But in MRI we are typically merely imaging protons which occur naturally in all elements and isotopes. Why is it that we observe no magnetic resonance phenomena in the elements? (except for hydrogen).

Wednesday, June 10, 2009

Humorous Aside: Thesis realism

Some jokes from PhDComics.com on keeping realistic thesis expectations.

Functional MRI

Functional MRI is an exciting idea: it allows us to create a map of how the brain responds when the person being imaged is subjected to some particular stimuli (say being shown a picture or told to perform a task). Functional MRI (fMRI) involves taking a measure of the amount of oxygen in a particular location of brain tissue. When a person’s mind activates with a particular thought/concept/action the activation can be measured by observing an increase in the amount of oxygen present (oxygen is delivered to activating regions by hemoglobin).

Tuesday, June 9, 2009

Measuring the strong force with MRI

MRI works because a proton that's in a strong magnetic field will polarize/align with the field and then behaves like a bell when it's hit with a radio wave (it rings back with another radio wave that we listen to in order to make an image).

Monday, June 8, 2009

Free will, predestiny or do we have to choose?

We all have the ability to use our memories to look back at past events. If we were to do so we would be aware that at one particular point in our past we chose to do some particular thing. In the present moment, free will implies that we have the ability to choose to do any particular thing.

Thursday, June 4, 2009

Physics: MRI a quark based dipole?

In MRI (magnetic resonance imaging) an image is obtained by placing a person in a strong magnetic field. The strong magnetic field causes the proton of a hydrogen atom to align with the field. A radio wave is applied to the person which causes the proton to be knocked out of alignment with the magnetic field. The strong magnetic field causes the proton to return to its original state, and this process of realigning lets off another (much smaller) radio wave, which we listen to. The final image is formed from measurements of the strength of these radio waves that emanate from hydrogen protons in the body.

Wednesday, June 3, 2009

The problems with currencies

As everyone is aware, the world's economic transactions are performed in a variety of different currencies. Currency traders share a generally accepted range of possible exchange rates for different currencies with respect to each other. If a new event occurs that appears to weaken a particular currency, currency traders are liable to buy and sell in a pattern that adjusts the exchange rate to devalue the currency.

Monday, June 1, 2009

The problems with mortgages

Economics is a fascinating science (physical scientists often look down upon the social sciences, however, social sciences are simply areas of scientific study that are affected by human behaviour – a fascinating challenge for the researcher).

Present law in Canada and the United States says that a banking institution can issue a mortgage while only actually having 10% of the amount of funds needed for the mortgage. The bank borrows the rest of the money from the central bank (a government agency: the Bank of Canada or the Federal Reserve in the USA). The banks are charged a remarkably low interest rate from the central bank and in turn charge YOU a higher interest rate on money they never even had!

Problems with economics policy

Currently the United States and Canada are funneling something like 60 billion dollars into General Motors (GM) and in exchange they are receiving 72.5% ownership of the company. The company has recently announced that it has over 170 billion dollars in debts. So the Canadian and US governments have just paid 60 billion dollars for the privilege of owing another 125 billion dollars (72.5% of 170 billion). GM will use $4-billion of the Canadian loans to address the shortfall in its pension plans. In addition, the company will inject $200-million into the pension plans over the next five years, making them fully solvent." So part of the plan that the government has funded is to provide GM with loans and GM will use 4 billion dollars of the Canadian loans to pay the pensions of former employees, and GM plans to 'fix' its pension problems by investing only 40 million dollars per year to make "them fully solvent" (ie. economically healthy). This is preposterous! How could 40 million per year fix a problem that needs 4 billion dollars right now?!

Wednesday, May 27, 2009

The Bohring model of the atom

It is kind of weird that we use the Bohr model of the atom, a man who advocated that quantum mechanics as a theory was complete (despite all its partially explained weirdness - presumably he felt it meshed well with his model of the atom).

Tuesday, May 26, 2009

Humorous Aside: God spawns the peer review process

A hilarious comic from the farside on God.

The weight of an electron

One of the main experiments to determine the weight of an electron in an educational physics class involves balancing a metal beam partially inside a solenoid (inductor – a big cork screw of tightly wrapped wire). The problem with this is that the force applied by the solenoid is dependent on the type and orientation of the metal balance beam inside core of the solenoid.

The other main way to measure the weight of the electron is by Thompson's charge-to-mass ratio experiment.

Friday, May 22, 2009

Funding for Scientific Research

Granting agencies disperse funds allocated for science which usually comes from public and charitable money. Private industry also funds scientific research, however it is typically heavily biased towards creating a new product or process that could be profitable. Unfortunately, granting agencies are also inclined to award funds to research that could lead to a new profitable product or process. This occurs by the very nature of the overly commercialized society in which we live – if scientific research is going to affect humanity for the better it is assumed that science will do so by creating a new invention that will have to become a commercial product – thus biasing scientific funding towards more commercializable endeavours.

Tuesday, May 12, 2009

Humorous Aside: Those quirky quarks

If you ever wanted evidence that particle physicists are confused about the physics of very small things then go to wikipedia and read the article that describes the nature of matter. Where matter is made of elements made up of protons, electrons and neutrons. Protons and neutrons are made up of quarks. And if you want an explanation of what a quark is, suddenly you’re reading about something called color charge and color confinement - weirdly arbitrary words when trying to describe something fundamental to the universe.

Tuesday, May 5, 2009

Who needs science when we have automatic-science!

So a few years ago some computer science students made a new computer program that will automatically create a scientist's research paper complete with text, figures, tables, methods, results etc. The papers are filled up with lots of technical terms and a lot of nonsense.

Sunday, April 26, 2009

Women in Science

While women’s rights have lead to amazing strides for women in science, unfortunately, those who do choose the field may still have to put up with chauvinism and exclusionary attitudes.

Tuesday, April 21, 2009

Humorous Aside: Job Satisfaction

I did a quick job satisfaction survey, check out the plot below.

Humorous Aside: The significance of beer and statistics

Did you know that scientists regularly require each other to show that their experiments are ‘significant’? This is typically done with a particular test (nerd alert! the t-test) that was developed over 100 years ago in a Guinness beer factory. The test was created long before computers but everyone still uses it despite the fact that if you collect many more samples than you could have by hand, the test will almost certainly give you the ‘significance’ that you’re looking for in your experiments.

Humorous Aside: Slow peer review

A colleague of mine made an important point on peer review: it takes so long for a typical peer-reviewed journal paper to get published that by the time it reaches publication, state-of-the-art research is often no longer state-of-the-art. As my colleague points out this long turn around time also forces many researches to repeat the same work of others simply because they don’t have access to the other researcher’s work!

Sunday, April 19, 2009

Peer Review

One of my main complaints with the world of science is that to advance one’s career, one must accumulate peer-reviewed journal publications. While having research articles reviewed by fellow specialist scientists clearly helps maintain a higher level of research paper quality, the present peer-review system is severely biased. 

Saturday, April 18, 2009

Humorous Aside: Career training vs. pay

For this site's first tidbit of the funnier side of science I provide for you a carefully researched and crafted plot of how much education/job training is needed compared with the pay for a variety of jobs. Note the awkward position scientists take: the gargantuan amounts of job training is not matched by a corresponding rise in pay – this didn’t bother me in the least when I signed up for graduate school, but now that I’m burdened down with debts I’ve got a bit of a different perspective.